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Related Concept Videos

Peptide Bonds02:43

Peptide Bonds

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A peptide bond covalently attaches amino acids through a dehydration reaction. One amino acid's carboxyl group and another amino acid's amino group combine, releasing a water molecule. The resulting bond is the peptide bond. The products that such linkages form are peptides. As more amino acids join this growing chain, the resulting chain is a polypeptide. Each polypeptide has a free amino group at one end. This end has the N-terminal, or the amino-terminal, and the other end has a free...
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Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors
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Isomerization kinetics of AT hook decapeptide solution structures.

Emily R Schenk1, Mark E Ridgeway, Melvin A Park

  • 1Department of Chemistry and Biochemistry, Florida International University , 11200 SW Eighth Street, AHC4-233, Miami, Florida 33199, United States.

Analytical Chemistry
|December 25, 2013
PubMed
Summary
This summary is machine-generated.

High mobility group protein A2's (HMGA2) AT hook peptide (ATHP) exhibits structured conformational dynamics. Trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) revealed key factors influencing its gas-phase structure and stability.

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Area of Science:

  • Biochemistry
  • Biophysics
  • Analytical Chemistry

Background:

  • High mobility group protein A2 (HMGA2) is implicated in various physiological processes, including oncogenesis and stem cell biology.
  • HMGA2 possesses DNA-binding motifs crucial for its function.
  • The third DNA-binding motif, the AT hook, is essential for HMGA2's interaction with DNA.

Purpose of the Study:

  • To investigate the conformational dynamics of the AT hook peptide (ATHP) from HMGA2.
  • To understand how solvent state influences the peptide's structure in the gas phase.
  • To elucidate the factors governing conformational interconversions in ATHP.

Main Methods:

  • Trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) was employed to analyze ATHP.
  • Electrospray ionization was used to generate ions from ATHP in different solvent states.
  • Ion mobility spectrometry (IMS) bands were analyzed to identify distinct conformers.

Main Results:

  • Solvent state distributions were maintained during ion formation, with multiple IMS bands observed for [M + 2H](2+) and [M + 3H](3+) charge states.
  • Conformational isomer interconversion rates were measured, providing insights into dynamic processes.
  • Protonation site, proline conformation, and side chain orientation were identified as critical for conformational changes.
  • ATHP demonstrated a structured nature from solution to the gas phase, with conformer stability correlating to relative abundances.

Conclusions:

  • The AT hook peptide (ATHP) exhibits significant structural organization even in the gas phase.
  • Protonation and proline conformations play key roles in the conformational dynamics of ATHP.
  • The most stable gas-phase conformation of ATHP ([M + 2H](2+)) resembles the structure observed when bound to AT-rich DNA regions.